Notices of courses, meetings, workshops, etc.

Online morphometrics course, Univeristy of Manchester. 6 November to 15 December 2017
Course content:
  • Data acquisition: the kinds of data and the equipment used to collect them.
  • Definitions of size and shape
  • Geometric methods to characterise shape from a configuration of landmark points (Procrustes superimposition)
  • Statistics of variation, scatter plots, basic multivariate statistics
  • Principal component analysis
  • Measurement error and outliers
  • Shape transformations and 'warping' -- the thin plate spline
  • Analysis of outline shapes
  • Distinguishing between groups (taxonomy, clinical diagnosis, etc.)
  • Allometry and size correction
  • Influence of external factors on shape (ecomorphology, dose-response studies)
  • Symmetric forms and measurement of asymmetry.
  • Morphometric inferences on developmental processes
  • Morphological integration and modularity
  • Genetics of shape: analyses of resemblance between relatives, QTL analyses.
  • Phylogeny: examining the history of evolutionary changes of shape

Practice examples: As far as possible, practical exercises are provided to accompany the course content. These practice exercises consist of data sets and explanations on how to run the respective analyses using the MorphoJ software (http://www.flywings.org.uk/MorphoJ_page.htm). Participants who already have their own data are encouraged to use those and to discuss them as part of the course. I hope there will be a bit of a 'workshop' feel to the course unit.

Group work: Participants will work in small groups to prepare web presentations of possible morphometric studies (wikis prepared by the groups). This activity stimulates discussion and provides a broad overview of the broad range of questions that can be addressed with morphometric methods.

Further information on the course and a link to the registration page can be found on the following we site: http://www.flywings.org.uk/MorphoCourse

Registration uses the university's e-store, which can process automatic *payments by credit card or debit card*. The deadline for registration via this site is the *20 October 2017*.

The direct link to the e-store is this: http://estore.manchester.ac.uk/short-courses/faculty-of-biology-medicine-and-health/school-of-biological-sciences/analysis-of-organismal-form

The fee for the course is GBP 350.00.

If you cannot pay by credit or debit card, or *if you require a formal invoice* (e.g. for reimbursement by your institution), you need to contact the Short Course Office in our faculty via this E-mail: ShortCourses-biosciences@manchester.ac.uk If you need to use this option, please do so as soon as possible, but definitely *well before October*.

Course From Phenotype to Genotype: The Genetic Basis of Shape, Jan 23-26, Barcelona (Spain)

Registration is open for the course: "From Phenotype to Genotype: The Genetic Basis of Shape - 4th Edition"; January 23-26, 2018.

Instructors: Dr. Neus MartÈnez-Abadías (Centre for Genomic Regulation, Spain) and Dr. Nicolas Navarro (Ècole Pratique des Hautes Ètudes, France).

Site: Premises of Sabadell of the Institut Catalá de Paleontologia Miquel Crusafont (Barcelona, Spain).

Course Webpage: http://www.transmittingscience.org/courses/genetics-and-genomics/phenotype-genotype-genetic-basis-shape/

The aim of this course is to provide participants with an overview of quantitative genetics, with specific application to shape analysis and decomposition of phenotypic variation into components of genetic and environmental variation. The basic theoretical concepts of resemblance between relatives, heritability, estimates of selection, and geometric morphometrics will be introduced. Practical lessons will enable participants to learn to use user-friendly (and not so user-friendly) software packages to estimate heritability, phenotypic and genetic variance covariance matrices, response to hypothetical selection, actual selection and QTL mapping.

Participants are encouraged to bring their own data for analysis and discussion in the course. Morphometric data involves any kind of quantitative shape data collected on individuals, such as linear measurements and/or 2D or 3D landmark coordinates. Pedigree files usually consist of text files with a list of three columns (individual ID, father ID, mother ID). Specific details about formatting these files will be provided during the practical lessons.

This course is co-organized by Transmitting Science and the Institut Catalá de Paleontologia M. Crusafont. Places are limited and will be covered by strict registration order.

Soledad De Esteban-Trivigno,PhD., Scientific Director, Transmitting Science, www.transmittingscience.org

Geometric Morphometrics Using R (GMMR01). 19 to 23 February 2018

Link: https://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/

This course is being delivered by Prof. Dean Adams, Prof. Michael Collyer and Dr. Antigoni Kaliontzopoulou

This course will run from 19th - 23rd February 2018 at Margam Discovery Centre, Wales, UK.

The field of geometric morphometrics (GM) is concerned with the quantification and analysis of patterns of shape variation, and its covariation with other variables. Over the past several decades these approaches have become a mainstay in the field of ecology, evolutionary biology, and anthropology, and a panoply of analytical tools for addressing specific biological hypotheses concerning shape have been developed. The goal of this is to provide participants with a working knowledge of the theory of geometric morphometrics, as well as practical training in the application of these methods.

The course is organized in both theoretical and practical sessions. The theoretical sessions will provide a comprehensive introduction to the methods of landmark-based geometric morphometrics, which aims at providing the participants with a solid theoretical background for understanding the procedures used in shape data analysis. Practical sessions will include worked examples, giving the participants the opportunity to gain hands-on experience in the treatment of shape data using the R package geomorph. These sessions focus on the generation of shape variables from primary landmark data, the statistical treatment of shape variation with respect to biological hypotheses, and the visualization of patterns of shape variation and of the shapes themselves for interpretation of statistical findings, using the R language for statistical programming. While practice datasets will be available, it is strongly recommended that participants come with their own datasets.

Note: Because this is a geometric morphometrics workshop in R, it is required that participants have some working knowledge in R. The practical sessions of the course will focus on GM-based analyses, and not basic R user-interfacing. It is therefore strongly recommended that participants refresh their R skills prior to attending the workshop.

Course Programme

Sunday 5th Meet at Millport field centre at approximately 18:30.

Monday 6th - Classes from 09:00 to 17:30
1: Morphometrics: History, Introduction and Data Types
2: Review of matrix algebra and multivariate statistics
3: Superimposition
4: Software demonstration and lab practicum
 
Tuesday 7th - Classes from 09:00 to 17:30
1: Shape spaces, shape variables, PCA
2: GPA with semi-landmarks
3: Shape covariation
4: Software demonstration and lab practicum
 
Wednesday 8th - Classes from 09:00 to 17:30
1: Phylogenetic shape variation
2: Group Differences & Trajectory Analysis
3: Allometry
4: Software demonstration and lab practicum
 
Thursday 9th - Classes from 09:00 to 17:30
1: Assymetry
2: Missing Data
3: Integration and Modularity
4: Disparity
5: Software demonstration and lab practicum
 
Friday 10th - Classes from 09:00 to 16:00
1: Future Directions
2: Lab Pacticum
3: Student Presentations

Please send inquiries to oliverhooker@prstatistics.com or visit the website www.prstatistics.com

Geometric Morphometrics course. 5 to 9 March 2018 in Berlin.

Instructor Dr. Carmelo Fruciano (Queensland University of Technology (Brisbane, Australia)).

OVERVIEW Geometric morphometrics has become a standard in biological research because it combines statistical rigour and ease of interpretation. Through geometric morphometrics, biological form is quantified, analysed and the results are expressed as easily interpretable and visually impactful shape changes. This course covers the main common practices of modern geometric morphometrics, including: acquiring data, analysing it, visualizing and interpreting the results.

FORMAT The course will be delivered over five days and will comprise both lectures and hands-on sessions. The lectures will cover both basic theoretical aspects and their practical implementation in research practice and software. During the hands-on sessions, the attendees will have the chance of both using example datasets and applying the knowledge acquired to their own data. The course will be focused mainly on 2D data and on easy-to-use software with graphical user interface to maximize the ability to understand concepts and apply them. However, some information on 3D data and on R implementations will be provided, as appropriate.

TARGET AUDIENCE This course is aimed at beginners and intermediate users. In other words, it is aimed at researchers who intend to use geometric morphometrics or who have started performing geometric morphometric analyses but feel they need a more structured background.

REQUIREMENTS Attendees should have a background in biology and a basic understanding of statistical

PROGRAM

5 March 2018

    Geometric morphometrics: overview and potential applications:
  • Traditional and geometric morphometrics
  • An overview of common analyses
  • Examples of geometric morphometrics applied to biological problems
    From biological objects to numerical representation:
  • Overview of typical devices used to digitalise biological objects
  • Landmarks, semilandmarks, outlines and surfaces - different types of geometric morphometric data
  • Most commonly used geometric morphometric software
  • Data quality, most common pitfalls in study design and data acquisition

6 March 2018

Generalized Procrustes analysis (GPA) - the core of most geometric morphometrics:

Principal component analysis (PCA)

    Comparing groups:
  • Between-group PCA
  • Canonical variate analysis (CVA)
  • Tests of difference in means

7 March 2018

    Co-variation between size and shape:
  • Allometry, regression and general linear models
    Co-variation between shapes:
  • Partial least squares analysis (PLS)
  • Modularity and integration

8 March 2018

    Combining analyses in a basic workflow:
  • Preliminary assessment of data quality
  • Typical basic workflow

Expanding the basic workflow: variation in geographic space

Expanding the basic workflow: association between shape and environmental variables

9 March 2018

Expanding the basic workflow: elements of phylogenetic comparative analyses

Review and open discussion

Presentation of attendees' analyses on their own data

Please visit our website to get more information about the course: https://www.physalia-courses.org/courses-workshops/course22/

Here is the full list of our courses and Workshops: https://www.physalia-courses.org/courses-workshops/

Carlo Pecoraro, Ph.D, Physalia-courses DIRECTOR, info@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses

https://groups.google.com/forum/#!forum/physalia-courses

The 7th edition of the course "3D Geometric Morphometrics" has opnened registration. Dates: December 11th-15th, 2017
Instructor: Dr Melissa Tallman (Grand Valley State University, USA).

Place: Facilities of the Institut Català de Paleontologia Miquel Crusafont,,C/ de l'Escola Industrial, n⁰ 23 08201 Sabadell, Barcelona.

Registration and more info: http://www.transmittingscience.org/courses/geometric-morphometrics/3d-geometric-morphometrics/

PROGRAM:

Types of data acquisition: Using a microscribe. Collecting CT scans & Surface Scans. - Demonstration of Stratovan Checkpoint.

Brief Review of Fundamentals of Morphometrics: - How to choose landmarks. - Generalized Procrustes Analysis. - Other types of alignment. - Thin plate spline warping. Processing Microscribe data. - Using DVLR to merge two views. - Using resample to resample a line. Using Landmark Editor to collect data on surfaces. - Sliding semi-landmarks (using R geomorph package).

  • How to do a precision test on 3D data.
  • Data exploration: PCA analyses: Using Morphologika. Using MorphoJ. Between-group PCAs. PCAs in Procrustes form space.
  • Visualizing shape change: Using MorphoJ in conjunction with Landmark Editor. Making calculations and visualizing shape changes in PCA morphospace. Calculating PCA scores post hoc.
  • Data exploration: Regressions. Visualizing change that is associated with size (MorphoJ). Removing change associated from size from your data (MorphoJ). Common allometric trajectories. Comparing vector directions. Extracting linear dimensions from 3D data and using them as covariates.
  • Data exploration: PLS analyses. Using MorphoJ to mean center (or not). Visualizing shape change in Landmark editor.
  • Data exploration: Phylogeny. Visualizing shape changes in MorphoJ along a tree. Importing covariates and visualizing shape change associated with taxonomy (using MorphoJ). Creating a phyomorphospace. Correcting for phylogeny in PCA.
  • Data interpretations: Using mean configurations (PAST) and Procrustes distances. Minimum spanning trees. Variability within a sample (comparing fossil distributions to extant distributions).
  • Retrodeformation.
This course is organized by Transmitting Science, the Institut Català de Paleontologia.


Rohlf medal
The first presentation of the Rohlf Medal was made to Fred L. Bookstein on Monday, October 24, 2011 at Stony Brook University. The 2013 recipient was Paul O'Higgins. The presentation was made on October 24, 2013. The title of his lecture was "The measure of things: pattern, process and morphometry". The 2015 recipient was Benedikt Hallgrímsson. It was presented on October 26, 2015 at Stony Brook University. The 2017 recipient will be Dennis Slice. More information about the awards including photos and links to the videos of the lectures are available here.

Nominations for the 2019 award can be made here - but not until January 2019. Repeat nominations do not need to include the full package of reprints and letters of reccomendation - just a letter making the case for the nominee in 2019.

Tax deductable donations to the Rohlf Medal fund can be made securely through the Stony Brook Foundation website.


Please notify me of any courses, meetings, or workshops so that they can be added to this list.
Archive of information about prior workshops.

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